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MCL coexpression mm9:814: Difference between revisions

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{{MCL_coexpression_mm9
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on=GO:0016070;RNA metabolic process;0.0150867558753302;53890,224902,245688,66880,238831!GO:0005634;nucleus;0.0150867558753302;53890,224902,245688,66880,238831!GO:0003723;RNA binding;0.0150867558753302;53890,224902!GO:0010467;gene expression;0.0150867558753302;53890,224902,245688,66880,238831!GO:0003676;nucleic acid binding;0.0150867558753302;53890,224902,233833,66880!GO:0005681;spliceosome;0.0150867558753302;238831!GO:0043229;intracellular organelle;0.0150867558753302;53890,224902,245688,233833,66880,238831!GO:0043226;organelle;0.0150867558753302;53890,224902,245688,233833,66880,238831!GO:0006139;nucleobase, nucleoside, nucleotide and nucleic acid metabolic process;0.0178250023094147;53890,224902,245688,66880,238831!GO:0016581;NuRD complex;0.0257457024294881;245688!GO:0044424;intracellular part;0.035962871102759;53890,224902,245688,233833,66880,238831!GO:0044428;nuclear part;0.035962871102759;245688,238831!GO:0005622;intracellular;0.0388715845836407;53890,224902,245688,233833,66880,238831!GO:0044446;intracellular organelle part;0.0388715845836407;245688,233833,238831!GO:0044422;organelle part;0.0388715845836407;245688,233833,238831!GO:0006396;RNA processing;0.0388715845836407;53890,238831!GO:0043283;biopolymer metabolic process;0.0388715845836407;53890,224902,245688,66880,238831!GO:0043231;intracellular membrane-bound organelle;0.0388715845836407;53890,224902,245688,66880,238831!GO:0043227;membrane-bound organelle;0.0388715845836407;53890,224902,245688,66880,238831!GO:0000118;histone deacetylase 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|gostat_on_MCL_coexpression=GO:0016070;RNA metabolic process;0.0150867558753302;53890,224902,245688,66880,238831!GO:0005634;nucleus;0.0150867558753302;53890,224902,245688,66880,238831!GO:0003723;RNA binding;0.0150867558753302;53890,224902!GO:0010467;gene expression;0.0150867558753302;53890,224902,245688,66880,238831!GO:0003676;nucleic acid binding;0.0150867558753302;53890,224902,233833,66880!GO:0005681;spliceosome;0.0150867558753302;238831!GO:0043229;intracellular organelle;0.0150867558753302;53890,224902,245688,233833,66880,238831!GO:0043226;organelle;0.0150867558753302;53890,224902,245688,233833,66880,238831!GO:0006139;nucleobase, nucleoside, nucleotide and nucleic acid metabolic process;0.0178250023094147;53890,224902,245688,66880,238831!GO:0016581;NuRD complex;0.0257457024294881;245688!GO:0044424;intracellular part;0.035962871102759;53890,224902,245688,233833,66880,238831!GO:0044428;nuclear part;0.035962871102759;245688,238831!GO:0005622;intracellular;0.0388715845836407;53890,224902,245688,233833,66880,238831!GO:0044446;intracellular organelle part;0.0388715845836407;245688,233833,238831!GO:0044422;organelle part;0.0388715845836407;245688,233833,238831!GO:0006396;RNA processing;0.0388715845836407;53890,238831!GO:0043283;biopolymer metabolic process;0.0388715845836407;53890,224902,245688,66880,238831!GO:0043231;intracellular membrane-bound organelle;0.0388715845836407;53890,224902,245688,66880,238831!GO:0043227;membrane-bound organelle;0.0388715845836407;53890,224902,245688,66880,238831!GO:0000118;histone deacetylase complex;0.0403579234012077;245688!
|ontology_enrichment_celltype=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0004177!2.49e-15!29;UBERON:0005057!2.49e-15!29;UBERON:0000153!1.68e-13!43;UBERON:0002370!3.21e-13!23;UBERON:0000974!3.21e-13!23;UBERON:0004807!3.21e-13!23;UBERON:0005058!3.21e-13!23;UBERON:0003351!3.21e-13!23;UBERON:0009113!3.21e-13!23;UBERON:0003295!3.21e-13!23;UBERON:0009722!3.21e-13!23;UBERON:0005562!3.21e-13!23;UBERON:0007690!3.21e-13!23;UBERON:0003408!5.82e-13!24;UBERON:0007811!4.78e-12!36;UBERON:0006562!6.51e-12!24;UBERON:0001557!6.51e-12!24;UBERON:0001042!6.51e-12!24;UBERON:0008814!6.51e-12!24;UBERON:0009145!6.51e-12!24;UBERON:0000077!1.28e-11!35;UBERON:0002390!4.00e-10!45;UBERON:0003061!4.00e-10!45;UBERON:0002193!2.19e-09!48;UBERON:0002405!2.19e-09!48;UBERON:0000072!4.43e-09!27;UBERON:0000065!2.43e-08!41;UBERON:0001004!2.59e-08!42
|tfbs_overrepresentation_for_novel_motifs=0.93395,0.227469,1.58148,0.394491,0.227651,0.40827,0.495658,0.146465,0.154135,0.904288,2.00501,0.484001,2.04018,0.507558,0.24249,0,0.696644,0.22065,0.829774,0.0703872,0.296085,1.09871,2.18306,0.226287,0.337218,0.534339,0.128175,0.428336,0.739731,0.319094,1.06602,0.796599,1.82817,0.364174,0.242923,1.0491,2.5174,2.09626,0.191662,0.167387,0.224094,1.07677,0.163087,0.244285,0.536558,0.998423,1.49936,1.12809,0.0330279,0.745859,0.679429,2.35985,0.30602,0.937018,0.954342,0.514504,0.279148,0.471658,0.12126,2.20234,0.776777,0.569793,0.163832,0.668331,2.24453,0.708248,1.08987,1.43807,0.772155,1.29123,0.840217,0.151245,1.14319,0.987652,1.22652,0.349958,0.113315,0.607043,0.759798,0.299972,0.152219,0.713779,0.568383,0.14134,0.873141,2.22499,0.231102,0.319367,1.50944,1.60001,1.15927,0.878077,0.809272,0.232894,0.188213,0.17334,0.14449,1.90157,1.49989,0.987389,0.210602,0.796322,0.919715,0.680015,0.678976,2.82314,1.74861,1.11973,1.48974,1.46548,0.348012,0.921485,0.814064,2.02173,1.16629,0.222515,0.795864,0.398075,0.697928,0.207304,0.993019,0.647706,0.536114,0.606154,1.22022,0.763454,0.503569,1.88204,1.08836,0.235546,0.90286,1.00644,1.05894,0.527782,1.18781,0.0467191,0.362565,0.421136,1.13883,1.96797,1.5682,1.09456,0.547855,0.806961,0.672593,0.420221,0.621266,1.92834,0.364791,1.88479,1.10522,0.659481,0.938577,0.527659,1.3067,1.01974,0.561556,0.253271,0.352329,0.362302,1.1483,0.872292,0.763895,0.914544,0.669337,0.519673,0.209556,0.482466,1.31706
}}

Latest revision as of 15:56, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr13:105018882..105018908,-p1@Ppwd1
Mm9::chr17:33822331..33822355,-p1@Hnrnpm
Mm9::chr17:56723930..56723991,-p1@Safb2
Mm9::chr3:66789622..66789662,+p2@Rsrc1
Mm9::chr5:114221652..114221668,-p1@Sart3
Mm9::chr5:130007098..130007128,+p1@Sfswap
Mm9::chr7:130267686..130267737,+p1@Tnrc6a
Mm9::chr7:52651042..52651089,-p1@Snrnp70
Mm9::chrX:159198320..159198347,+p2@Rbbp7


Enriched pathways on this co-expression cluster<b>Summary:</b><br>Canonical pathway gene sets were compiled from Reactome, Wikipathways and KEGG. For the major signaling pathways, the transcriptionally-regulated genes (downstream targets) were obtained from Netpath. Combined, the canonical pathways and downstream targets totaled 489 human gene sets. The corresponding M. musculus gene sets were inferred by homology using the HomoloGene database. Enrichment for each of the canonical 489 pathways and gene sets included in the co-expression cluster was assessed by the hypergeometric probability. The resulting P values were also then adjusted by the Benjamini-Hochberg method for multiple comparisons.<br><b>Analyst: </b>Emmanuel Dimont<br><br>link to source dataset<br>data

GO IDGO nameFDR corrected p-value
GO:0016070RNA metabolic process0.0150867558753302
GO:0005634nucleus0.0150867558753302
GO:0003723RNA binding0.0150867558753302
GO:0010467gene expression0.0150867558753302
GO:0003676nucleic acid binding0.0150867558753302
GO:0005681spliceosome0.0150867558753302
GO:0043229intracellular organelle0.0150867558753302
GO:0043226organelle0.0150867558753302
GO:0006139nucleobase, nucleoside, nucleotide and nucleic acid metabolic process0.0178250023094147
GO:0016581NuRD complex0.0257457024294881
GO:0044424intracellular part0.035962871102759
GO:0044428nuclear part0.035962871102759
GO:0005622intracellular0.0388715845836407
GO:0044446intracellular organelle part0.0388715845836407
GO:0044422organelle part0.0388715845836407
GO:0006396RNA processing0.0388715845836407
GO:0043283biopolymer metabolic process0.0388715845836407
GO:0043231intracellular membrane-bound organelle0.0388715845836407
GO:0043227membrane-bound organelle0.0388715845836407
GO:0000118histone deacetylase complex0.0403579234012077



Relative expression of the co-expression cluster over median <br>Analyst:




Enriched sample ontology terms on this co-expression cluster<b>Summary:</b>To summarize promoter activities (expression profile of a TSS region) across ~1000 samples, we performed enrichment analysis based on FANTOM5 Sample Ontology (FF ontology). The question here is “in which type of samples the promoter is more active”. To answer this question, we compared expressions (TPMs) in the samples associated with a sample ontology term and the rest of the samples by using the Mann-Whitney rank sum test. To summarize ontologies enriched in this co-expression cluster, we ran the same analysis on an averaged expression profile of all promoters that make up. <b>Analyst:</b> Hideya Kawaji <br><br>links to source dataset<br><br><br>uberon_data<br><br>

Uber Anatomy
Ontology termp-valuen
hemopoietic organ2.49e-1529
immune organ2.49e-1529
anterior region of body1.68e-1343
thymus3.21e-1323
neck3.21e-1323
respiratory system epithelium3.21e-1323
hemolymphoid system gland3.21e-1323
pharyngeal epithelium3.21e-1323
thymic region3.21e-1323
pharyngeal gland3.21e-1323
entire pharyngeal arch endoderm3.21e-1323
thymus primordium3.21e-1323
early pharyngeal endoderm3.21e-1323
gland of gut5.82e-1324
craniocervical region4.78e-1236
pharynx6.51e-1224
upper respiratory tract6.51e-1224
chordate pharynx6.51e-1224
pharyngeal arch system6.51e-1224
pharyngeal region of foregut6.51e-1224
mixed endoderm/mesoderm-derived structure1.28e-1135
hematopoietic system4.00e-1045
blood island4.00e-1045
hemolymphoid system2.19e-0948
immune system2.19e-0948
segment of respiratory tract4.43e-0927
respiratory tract2.43e-0841
respiratory system2.59e-0842


TFBS overrepresentation<b>Summary:</b>The values shown are the p-values for overrepresentation of the motif in this coexpression cluster. So a small p-value means a strong overrepresentation. <b>Analyst:</b> Michiel de Hoon <br><br>link to source data <br> Novel motifs <br>data <br><br> Jaspar motifs <br>data

Novel motifs




JASPAR motifs


Motifs-log10(p-value)
MA0003.10.904101
MA0004.10.394951
MA0006.10.670874
MA0007.10.38073
MA0009.10.82278
MA0014.10.119217
MA0017.10.26239
MA0019.10.642876
MA0024.10.779446
MA0025.11.05446
MA0027.12.46647
MA0028.12.77501
MA0029.10.757957
MA0030.10.764448
MA0031.10.729293
MA0038.10.534262
MA0040.10.835181
MA0041.10.323687
MA0042.10.311486
MA0043.10.918718
MA0046.10.858391
MA0048.11.47862
MA0050.10.431976
MA0051.10.542972
MA0052.10.84317
MA0055.10.221677
MA0056.10
MA0057.10.258928
MA0058.10.823526
MA0059.10.316585
MA0060.10.9744
MA0061.10.56663
MA0063.10
MA0066.10.523573
MA0067.11.16502
MA0068.10.563625
MA0069.10.843506
MA0070.10.833895
MA0071.10.431174
MA0072.10.825495
MA0073.10.513723
MA0074.10.488775
MA0076.12.14767
MA0077.10.804033
MA0078.10.575205
MA0081.10.338098
MA0083.10.917931
MA0084.11.49188
MA0087.10.87515
MA0088.10.18495
MA0089.10
MA0090.10.362551
MA0091.10.407455
MA0092.10.362847
MA0093.10.709711
MA0095.10
MA0098.10
MA0100.10.477594
MA0101.10.867731
MA0103.10.272167
MA0105.10.35523
MA0106.11.42499
MA0107.10.73569
MA0108.20.665343
MA0109.10
MA0111.10.375908
MA0113.10.555251
MA0114.10.19245
MA0115.10.921497
MA0116.10.238371
MA0117.10.88947
MA0119.10.868953
MA0122.10.909168
MA0124.11.11203
MA0125.11.03833
MA0130.10
MA0131.11.54167
MA0132.10
MA0133.10
MA0135.10.954884
MA0136.10.508047
MA0139.10.441109
MA0140.10.477483
MA0141.10.29014
MA0142.10.714976
MA0143.10.571221
MA0144.10.195095
MA0145.11.17902
MA0146.13.35461
MA0147.10.205697
MA0148.11.05634
MA0149.10.330018
MA0062.23.09014
MA0035.20.482026
MA0039.20.043355
MA0138.20.630612
MA0002.20.145685
MA0137.20.287486
MA0104.20.476119
MA0047.20.533516
MA0112.20.771888
MA0065.20.0545595
MA0150.10.380623
MA0151.10
MA0152.10.53362
MA0153.10.971406
MA0154.10.0809407
MA0155.10.490492
MA0156.11.39718
MA0157.10.683365
MA0158.10
MA0159.10.214506
MA0160.10.413266
MA0161.10
MA0162.11.22186
MA0163.11.53225
MA0164.10.508398
MA0080.20.737531
MA0018.20.51781
MA0099.20.624421
MA0079.20.811827
MA0102.21.5442
MA0258.10.533988
MA0259.10.571417
MA0442.10
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